The most obvious difference is the ends, which were quite different. The NP cars had normal 4/5 "S-corner" ends while the GN cars had inset 4/5 "S-corner" ends. Both cars had exposed lower trusses along the bottom sill. The ancient ATHEARN double sheathed box car kit is very similar to the NP box car.
I haven't seen the entire thread yet, but the reason the GN cars had "inset" ends is because the GN's cars are simply 1925 ARA box cars built to the prevailing dimensions of the late 1930s/early 1940s.